Mass defect information can be used to filter mass spectrometer data. However, most such methods typically use a mass defect based filtering window that does not scale with ion mass and/or does not include a statistical confidence performance measure. In such cases, the selected mass defect window is generally only optimal for a limited mass range. Various embodiments of the present teachings provide a statistical confidence value associated with the mass defect window selected and filter the data such that the window appropriately scales with the mass of the compound.